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Nucleic Acids Research Papers on Cancer Virtual Cohort, Single-Cell Cancer Expression, Variant Tools

Researchers from Peking University present an integrated web platform designed to bring together several types of molecular and clinical data generated through large efforts such as the Cancer Genome Atlas (TCGA) project and work done by the Clinical Proteomic Tumor Analysis Consortium (CPTAC). The tool — known as the "Cancer Virtual Cohort Discovery Analysis Platform," or CVCDAP — is designed as "an interactive and customizable toolbox off the shelf for cohort-level analysis of TCGA and CPTAC public datasets, as well as user uploaded datasets," they note. Along with options for generating virtual cohorts based on shared molecular or clinical features, the team touted the customizable tools included in CVCDAP for analyzing and comparing cancer datasets.

A team from the Princess Margaret Cancer Center, the Hospital for Sick Children, and other centers describe the "Cancer Single Cell Expression Toolkit," or CReSCENT — a scalable web resource housing standardized single-cell RNA sequencing data in a format that allows for analyses of tumor expression data and the addition of new scRNA-seq data. "While scRNA-seq data for tumor specimens are readily generated, subsequent analysis requires high-performance computing infrastructure and user expertise to build analysis pipelines and tailor interpretation for cancer biology," the researchers write. CReSCENT uses public datasets and preconfigured pipelines that are accessible to computational biology non-experts and are user-editable to allow optimization, comparison, and reanalysis for specific experiments."

Finally, Queen Mary University of London researchers report on updates to the online annotation tool SNPnexus. The latest version of the freely available web-based tool — used to find and characterize new and known single nucleotide changes, small insertions and deletions, and other variants in the human genome — includes broader annotations based on biological clues, pathway analysis options, cancer-focused variant tools, and faster computation times. With the inclusion of these and other updates, the authors suggest that "SNPnexus is the most comprehensive web-based application currently available and [the] new set of updates ensures that it remains a state-of-the-art tool for researchers."